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Subject: Bio-Eco/logy software tools/A few reviews
From: Aldo-Pier Solari <[log in to unmask]>
Reply-To:[log in to unmask]
Date:Sat, 28 Jun 1997 23:19:21 GMT

text/plain (1412 lines)

A  few  reviews   on   biology-ecology  related  software  tools.
[log in to unmask] does not endorse the use of  any  of
the   software   packages   listed   herein   unless   they   are
free/shareware  or self cost applications developed by scientists
for scientists.  Cheers, APS.

Dobson,Alan (1988): Acid-Base  Simulation.  (Wisc-Ware) [BIOLOGY,
CHEMISTRY, DOS<This program is the best I have ever seen in the
sense of simplicity.  There are two commands that I have not seen
in any other program - the first one  is  called  control  guided
tour  and  the  second is called the menu guided tour.  The first
shows automatically how to  perform  a simulation using the hints
s/he has in the program, and the other one shows a person who  is
unfamiliar  in  using  windows  or  a  mouse  how  to do so.  For
example, it demonstrates how to change  the size of the window or
how to close a window, etc.  Because of  these  two  commands,  I
think  there is no need for a teacher to show you how to use this
program.  I did know how to perform a simulation, but when I used
the control guided tour it  showed  me  exactly  how to do so.  I
strongly recommend this program for in class use by  students  of
any  classification.   However,  like the author said the student
should be familiar with  the  respiratory and the renal function.
Note: In my opinion  every  program  should  have  at  least  the
control  tour  guide so that if somebody has difficulty using the
program, s/he would not waste  so much time getting familiar with
the program if such commands existed.  (REVIEW  1:  RATING  =  9)
This  program  was  really easy to use.  The fact that it is used
under  windows  with  a  mouse  makes  all  the  commands  easily
accessible.  I thought the experiment was  neat and it did a good
job of demonstrating equations and graphs.   I  really  like  the
control guided tour.  These options allowed me as a naive user to
view different controls and there functions.  This feature really
helps the user be aware of and take advantage of every option the
software  has.   I think that the format of the software could be
applied to other programs in  order  to  make them easier to use.
In my opinion, this program could be  used  successfully  by  all
students.  (REVIEW 2: RATING = 8)>

SCIENCE STUDENTS (Supported by NSF Grant)

REVIEWER  1  - Azmy Ackleh REVIEWER 2 - Shannon Peak REVIEWER 3 -
Holly Gaff

For more information  contact:  Dr.   Louis  J. Gross Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]

Will,Ed  (1987):  ANIMAL   KINGDOM.    (Hypercard   application)
[BIOLOGY,  MAC,  TAXONOMY <This program is a very small program
that would have very limited  use.   The  basic uses that I could
see include a basic animal kingdom class to see how the taxonomic
structure is developed.  The program itself is not very friendly.
The user must know fully how to use HyperCard on the  Mac.   Even
then,  the program is not well labeled.  There doesn't seem to be
much extended use for this program.  (REVIEW 3: RATING = 4)>

SCIENCE STUDENTS (Supported by NSF Grant)

REVIEWER 1 - Azmy Ackleh REVIEWER  2  - Shannon Peak REVIEWER 3 -
Holly Gaff

For more information contact: Dr.   Louis  J.  Gross  Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]

Jeanne,Robert  (1988):  Ants.  (Wisc-Ware) [BIOLOGY, DOS-WINDOWS]
<Ants is an interactive  program  to study the system reliability
of different ant foraging strategies.  In this  program  you  are
asked  to  select  a  particular strategy and input the necessary
information for that strategy.   A  schematic for the strategy is
either drawn automatically or you are given  the  opportunity  to
design  one  yourself.   After  the  schematic has been drawn the
graph of the strategy  may  be  displayed.  This plots individual
reliability versus system reliability.  A max of five  plots  may
appear  on  the graph, after that the oldest one will be replaced
by the new one.   The  program  is  easy  to  use, but for better
understanding of the program you  should  be  familiar  with  ant
foraging and reliability theory.  The author suggests the reading
of  the  following  paper:  Joan  Herber, "Reliability Theory and
Foraging by Ants", J.Theor.  Bio., 1981, 89:175-189.  The program
requires Windows to run.  You cannot save a certain schematic for
a strategy you have chosen, also  you cannot print out a graph or
a schematic figure for the strategy you have chosen  or  clear  a
graph from a window.  (REVIEW 1: RATING = 4)

This  is very specific software that was designed specifically to
study the foraging strategies of ants.  The software is very user
friendly in the  fact  that  it  is  used  under  Windows and the
commands are really easy to understand.  I had no  problem  using
the  program,  and  I  think  that  even people with very limited
computer knowledge  could  use  it.   However,  the  program does
require previous knowledge of the subject  matter.   This  limits
the  use  of  the program because it cannot be used as a teaching
device.  The program  can  only  be  used to demonstrate specific
examples and supplement  what  has  already  been  learned.   The
program  also has no way to clear graphs, therefore the user must
continually look at five graphs  and  try  to figure out which is
the most recent.  This could present a problem especially if  the
graphs  vary  by  only  a small amount.  Also, there is no way to
save situations  you  create  or  print  graphs.   I  thought the
program would have been a lot more useful if there were  examples
already  loaded  onto  the system that you could experiment with.
The thing I liked  the  best  about  the  program  is the you can
design your own schematic- this was  easy  to  do  and  made  the
program interesting.  In my opinion, this software would be a lot
more  useful  if  explained  the  subject  matter as well as gave
examples.  (REVIEW 2: RATING = 4)>

SCIENCE STUDENTS (Supported by NSF Grant)

REVIEWER 1 - Azmy Ackleh REVIEWER  2  - Shannon Peak REVIEWER 3 -
Holly Gaff

For more information contact: Dr.   Louis  J.  Gross  Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]

Camazine,Scott (1990): Automata.  (Cornell University, Section of
Neurobiology  and Behavior) [CHAOS, MAC<This package includes a
number of files  of  different  chaos  images.   The package also
contains a program that will create random images.  This could be
useful  for  pattern  analysis.   I  am  not  sure  of  what  the
applications of this program  will  be,  but  it  has  some  nice
features and good graphics.  (REVIEW 3: RATING 7)>

SCIENCE STUDENTS (Supported by NSF Grant)

REVIEWER  1  - Azmy Ackleh REVIEWER 2 - Shannon Peak REVIEWER 3 -
Holly Gaff

For more information  contact:  Dr.   Louis  J. Gross Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]

Macey,Robert I;  Calley,John  N;  Curylo,Alex  T  (1991):  Axon.
(BioQUEST)   [ECOLOGY,   MAC  <A   simulation  of  the  classic
Hodgkin-Huxley (1952) model  for  axon excitation formulated from
their  voltage  clamp  measurements  upon  the  squid  Axon.   It
provides you with a simulated excised  peripheral  nerve  from  a
squid  and  allows  you  to  perform  experiments  by setting the
environment of axon and stimuli or  clamps applied to it and view
graphically  assorted  nerve  properties,  such   as   threshold,
refractory period, accommodation and summation.>

SCIENCE STUDENTS (Supported by NSF Grant)

REVIEWER  1  - Azmy Ackleh REVIEWER 2 - Shannon Peak REVIEWER 3 -
Holly Gaff

For more information  contact:  Dr.   Louis  J. Gross Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]

Frischknecht,Markus  (19--):  BIO-ESS.   (University  of   Berne,
Institute  of  Zoology,  Wohlenstrasse  50a, Switzerland, e-mail:
[log in to unmask]) [ECOLOGY, MAC <This  is a stack that
demonstrates some aspects of evolutionary stable strategies.  The
Hawk and the Dove have different strategies in a population model
in which species fight each other to get a resource.  Each time a
Hawk meets another Hawk they start risky fight.  The  probability
to  win  is  50%.   The  probability  to meet another Hawk is the
frequency  of  this  strategy  in  the  population.   But  if the
competitor is a Dove then the Hawk gets all the  resource.   When
two  Doves  meet they share the resource.  The game is fun, it is
user friendly and has option to change the model which calculates
the frequencies.  Graphics are  nice.   And the author states all
the limitations such as the variable "value" and "damage"  should
not  exceed 10 because the frequency becomes negative which makes
no sense, etc.  (REVIEW 2: RATING = 7)>

SCIENCE STUDENTS (Supported by NSF Grant)

REVIEWER 1 - Azmy Ackleh REVIEWER  2  - Shannon Peak REVIEWER 3 -
Holly Gaff

For more information contact: Dr.   Louis  J.  Gross  Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]

Odell,Garrett M; Segel,Lee  A  (1987):  Biograph.  (Cambridge New
York  New  Rochelle  Melbourne  Sydney)   [CALCULUS,   DIFFERENCE
<Biograph is an  interactive  program  that computes numerically,
then  graphs  solutions  to  systems  of  ordinary   differential
equations  (ODE's)  and  difference  equations.   The  program is
capable of solving systems  of  n simultaneous DE's or difference
equations.  Biograph is a menu driven program, but the menus  are
a little hard to understand.  For example, when you are in a menu
other  than  the  main  menu  you have no way of knowing that the
command F10 will return  you  back  to  the main menu.  Also, the
graphics are not very sophisticated.  For example, the  axes  are
not  marked  by the variable they represent.  There is also great
difficulty in creating your  own  file,  I  wasted  a lot of time
trying to create my own model and was unable  to  do  so.   (This
program  is not at all user friendly!) However, other than that I
think that the program is good.  It  has a lot of options such as
saving data to a file, retrieving data previously  saved,  output
data,  changing  parameters  in already existing models, changing
initial conditions, or determining the  limits  of the axes for a
graph.  You can also determine equilibrium points,  get  a  phase
plane,  and  graph  every  variable  versus  time  axis.  (REVIEW

This  software  was  very  hard  to  use.   To  begin  with,  the
descriptions  on the main menu are not very explanatory.  I had a
hard  time  relating  what  I  wanted  to  do  with  the  choices
represented on the menu.  I  even  looked at the user manual, but
it was very little help to me.  For example, when you are in  one
of  the submenus and press 'q' to quit, it does not return you to
the main menu, instead it returns  you  to a black screen with no
indication where the cursor is.  This was confusing to me, and  I
had to randomly press keys until I found out that you press enter
in  order  to  make  the  main  menu  appear.  When I retrieved a
document and had the program graph it  for me, I did like the all
the information available about the  graph,  but  I  thought  the
graph  itself  looked  plain  compared to software I have already
used.  In my opinion,  this  software  would be frustrating for a
naive user to work with.  When compared to Models or Phaser, this
software is easily the most difficult to execute and  work  with.
The  program  itself  would  be  good  to  solve differential and
difference equations  because  it  provides  the  user with great
options in order to examine  the  graphs  and  solutions  of  the
problems.   However, it requires a great deal of time in order to
be able to execute the program successfully.  (REVIEW 2: RATING =

For review refer to THE QUARTERLY REVIEW OF BIOLOGY December 1990
volume 65 page 539.>

SCIENCE STUDENTS (Supported by NSF Grant)

REVIEWER 1 - Azmy Ackleh REVIEWER  2  - Shannon Peak REVIEWER 3 -
Holly Gaff

For more information contact: Dr.   Louis  J.  Gross  Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]

Bergdoll,  S.  and  J.  Grethe (1991) BioSimPC, ver 2.0 (BASF-AG)

<This is a simulation  program  for  neurons.  The program allows
the user to input information about  the  types  of  neurons  and
synapses  to  be  simulated.   The user must know a lot about the
biology of neurons to  use  this  program.  The graphics are very
nice.  There is help available, but  again,  one  must  know  the
biology.   This package would be good for someone who knows about
nerves and wanted to  explore different nerve connections.  There
are some sample files, but a more structured example  would  have
been  very  helpful.  Overall, the program is well done and could
be very useful for certain fields.  (Review 3: Rating 6)>

SCIENCE STUDENTS (Supported by NSF Grant)

REVIEWER 1 - Azmy Ackleh REVIEWER  2  - Shannon Peak REVIEWER 3 -
Holly Gaff

For more information contact: Dr.   Louis  J.  Gross  Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]


Goburn,Alex (1990): BIOSIMS.  (130 Browood  # 621, FT Collins, Co
80521,  phone  (303)  221-9489)  [BIOLOGY,   ECOLOGY,   GENETICS,
POPULATION <The  programs  in BIOSIMS are very simple - each is
good only as an  introduction  to  the  subject.  For example the
Population Growth model contains only three models,  exponential,
logistic  and  growth with lags.  You have the option of changing
the parameters  such  growth  rate  initial  population, carrying
capacity and # of generations you want to simulate.  You have  no
way  of printing out the graphs other than print screen and there
is no on-line help.  In fact,  I have written a program doing the
same exact thing using MATLAB.  It took about an hour to do  that
so  I don't think it is very exciting.  The second program Action
Potential is also very simple.  The process is this: you enter an
initial membrane  potential  then  change  the membrane potential
with a stimulus.  You then observe the action potential  and  the
associated  Na+  K+  conductance change.  Again, there is no help
(which is probably not  needed  because of simplicity of program)
and no way of printing.  The third program Gene Plot is good only
for a classic population as the  author  said,  "in  the  classic
population  there  are only two alleles which may produce a total
of  three  different  genotypes.   In  this  model  phenotype  is
implicit and  selection  only  works  on  genotypes.  Although in
reality you can only select on phenotype this is a good model  to
understand  the  concept of " natural selection." Again there was
no way of printing.  In this program there was a help option, but
the problem is that if  you  chose  this option you can't quit in
the middle of the help menu you have to scroll through the  whole
thing  to  get  out.   Overall  these  programs  are good only as
introduction to these  subjects  though  they  are user friendly.

SCIENCE STUDENTS (Supported by NSF Grant)

REVIEWER  1  - Azmy Ackleh REVIEWER 2 - Shannon Peak REVIEWER 3 -
Holly Gaff

For more information  contact:  Dr.   Louis  J. Gross Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]

Dawkins,Richard (1987): Blind  Watchmaker.   (W.W.   Norton,  New
York)  [BIOLOGY,  GENETICS,  MAC<This is a really nice package.
It allows the user to set the mutation rate for a species.  There
are a number of different species that one could use.  All of the
species are merely graphics.   The  mutation  of the species is a
process of different symmetries.  The package is well written and
very friendly.  It is a nice graphics  display  that  allows  the
user to see the effect of mutation.  This program is a simple one
that  would  be  useful  in  a genetics class for seeing mutation
effects.  (REVIEW 3: RATING 9)>

SCIENCE STUDENTS (Supported by NSF Grant)

REVIEWER 1 - Azmy Ackleh REVIEWER  2  - Shannon Peak REVIEWER 3 -
Holly Gaff

For more information contact: Dr.   Louis  J.  Gross  Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]

Kreitzer,GP;   Borisyuk,RM   (1989):  Catching  Fish.   (Applied
Biomathematics) [ECOLOGY, SINGLE POPULATION, DOS<This is a game
of catching fish.  Each game  consist  of ten seasons of fishing,
and you can adjust the intensity of fishing at the start of  each
season.   One set consist of five games, but you can extend it to
ten games.  You can view previous games within a set by selecting
the "View Game" function.  You also have the option of saving any
interesting game on a disk.  You can restore them, as well as the
relevant parameters, and continue the game with these parameters.
For saving, loading  and  deleting,  select  the "File" function.
However, you can only save this information for one session-  you
lose  all  information  if  you  quit  the session.  If you over-
fished and caused the abundance to fall below the critical value,
the prompt  "Poor  fish!"  is  displayed  and  the  score will be
negative (i.e.  you doomed the population to die out).  A  simple
easy  game  to understand but in my opinion it fits more students
that are in high school.  (REVIEW 1: RATING = 7)

This  program  teaches the user the impact of fishing on the fish
population by making it a  game  the user can play.  The software
was really user friendly and  commands  were  easily  accessible.
The user can simply move to the command s/he wants with the arrow
keys and indicate this command by hitting enter.  I liked the way
that  the graph appeared as you were playing.  The only problem I
had with the game is  that  there  is  no way to save information
from one use to another.  In my opinion, this software  could  be
used  by anyone, and could prove informative if someone wanted to
learn the effects of  fishing  on  a fish population.  (REVIEW 2:
RATING = 7)>

SCIENCE STUDENTS (Supported by NSF Grant)

REVIEWER 1 - Azmy Ackleh REVIEWER 2 - Shannon Peak REVIEWER  3  -
Holly Gaff

For  more  information  contact:  Dr.  Louis J. Gross Mathematics
Department University of Tennessee Knoxville, TN 37996-1300 (615)
974-4295 (615) 974-6576 (FAX) [log in to unmask]


This is a nice program that allows the user to manipulate a model
of the sterile insect release method.  The program is easy to use.
There is on-line help available that is very useful.  The program
offers good graphic and verbal conclusions.  The problem is set up
with the user setting the parameters.  Then the solution is run one
generation at a time.  The program is useful for the model it is
designed for.  (REVIEW 3: RATING 7)


Marck,Christian (1990): DNA Strider 1.0.  (Institut de  Recherche
Fondamentale,  France)  [BIOLOGY,  GENETICS,  MAC <This program
allows the user  to  convert  potential  DNA sequences into their
respective proteins.  The program is not friendly at all.  I  had
a hard time figuring out what was going on.  There seems to be no
instructions included.  The program requires a DNA sequence to be
put  in.  This is a long and tedious process.  I did not see much
that was very useful in this program.  (REVIEW 3: RATING 2)>


Lapin,Lawrence  (1987):  Easystat.   (Harcourt  Brace  Jovanovich
Inc.)  [STATISTICS,  DOS<This is an easy software to understand
and to get familiar with.   The  main menu looks like this: "Main
Menu: File Edit Column Stat Utility Help Quit." Each of the above
options requires no background  to  understand  except  the  Stat
option.   Its  menu  looks like the following: Stat Menu: Summary
Hist Probability Regression ANOVA  Chi Std.Err Time Non-para.  In
order to use this menu you need to  understand  the  above  basic
statistical  terms.   This program has a lot of nice options such
as being able to fill a table randomly giving the upper and lower
limits.  You are able to edit a table, print out a table, graph a
column versus another, copy  one  column  to another, or delete a
column.  You also have a help screen.  You are  able  to  perform
arithmetic  operations  on  any  column  (add,  multiply, divide,
power, logarithm, etc.) In general, this  is a nice and easy that
need only elementary  background  in  statistics.   However,  the
graphics  are  not  very sophisticated, and they can sometimes be
confusing because they graph only  coordinates and do not connect
them.  Also, it doesn't give error messages when  you  enter  the
wrong input instead it freezes for some time and then comes back.
(REVIEW 1: RATING = 7.5)

This  program  is similar to a spread sheet with many statistical
applications.  For this reason,  I  think  that most people would
find it easy to use, especially if they have worked  with  spread
sheets  before.   The  menus  are  nice in the fact that when you
highlight a menu it  prints  underneath what options are included
in that menu.  This makes it easy to  access  whatever  operation
you want to perform.  I liked the various options the program had
concerning  the  manipulation  of data.  For example, I liked the
fact that you  can  randomly  fill  a  column  with data you have
already entered.  I  liked  the  fact  that  the  program  graphs
information  for  you, especially one column against another, but
the graphs are not very sophisticated.  I thought the statistical
options were very nice.  I feel  this software would be useful to
students who wanted to apply statistics to  real  situations.   I
think  that  it  could  be  used  with  a  class in order to help
students apply the  distributions  they  usually only read about.
It would also let them  compare  various  distributions.   In  my
opinion,  this software is simple to use and could very easily be
used by students taking statistics.   The only problem I had with
the program is that there are no  error  messages,  and  on  some
occasions  I found myself having accidentally escaped the program
before I realized what was going on.  (REVIEW 2: RATING =8)>


Exeter Software (1990):  Ecological  Computer  Games.  (100 North
Country  Rd.   Setauket,  NY)  [COMPETITION,  ECOLOGY,   MULTIPLE
can be a good lesson for  students.  They can explain how one can
choose a strategy in order for the  species  in  a  predator-prey
system  to  survive.   (For example, the fox and rabbit game.) In
the Hawk, Weasel and  Mice  game  the  speed  of the opponent was
always faster which made it difficult for me to win or  make  the
three  species  survive.   It was frustrating.  The same with the
Rabbit and Fox game.  However,  I  liked the Trout game the most.
I was able  to  crash  the  species  or  make  the  species  grow
logistically.   It  seemed  to me that the best strategy for this
game is to stay  on  the  surface  and  eat only insects.  A nice
thing about the three games are the graphs that show  the  change
of each species with time.  (REVIEW 1: RATING = 7)

 This  software teaches you about populations while also allowing
you to participate in a game.  I think the fact that the user can
play a game makes it more  appealing  to use.  The Trout game was
fun, but the other ones made it very difficult  to  win,  because
the  prey  and  the opponents move a lot faster than the predator
that is being manipulated  by  the  user.  The program was really
user friendly and easy to use.  It also offered good explanations
for what was happening and graphs.  The only  things  I  did  not
like  about  the  program was that once you start the program you
cannot quit without playing a round  nor can you change the speed
of the participants without quitting the program and starting  it
over.   In  general, I think that the program can teach a student
about how populations crash  or  thrive  based on energy and food
consumption while making it into a game.  (REVIEW 2: RATING = 7)>


Chariot Software Group  (1988):  Ecology  Stack,  Geology  Stack,
Science  Stack.   (CSG Pub Domain/ SW Library) [ECOLOGY, GEOLOGY,
MAC<Ecology Stack: This software is nothing but a tutorial disk
that presents ecological questions  and  topics on related talks,
maps, etc.  Geology Stack: Again this is a geological tutorial on
projections of maps etc.  Science Stack: It contains  a  demo  of
Macrograde a software that is used by instructors to keep records
of  students' grades etc.  It also contains nice Astronomy slides
and a demo of the software  Physics test.  It is only a tutorial.


Host,E; Rauscher,M; Iserbrands,J; Dickmann,D; Dickson,R;  Crow,T;
Michael,D  (1990):  Ecophys.   (U.S  Dept.   of Agriculture, 1992
Folwell Ave.,  St.   Paul,  Minnesota  55108>  [BIOLOGY, ECOLOGY,
PHYSIOLOGY, DOS<This is an explanatory whole-tree process model
that simulates the growth of  Populus  during  the  establishment
year.   Ecophys  allows  the  user  to change physiological based
factors that influence the growth  of  Populus.  It is helpful to
know how these factors affect  growth  in  order  to  identify  a
genetic  selection  criteria, which may be used for the selection
and breeding of  poplar  clones.   The  program consists of three
primary modules which control the actual simulation  and  several
supporting  modules which allow physiological, environmental, and
simulation parameters to be modified.   In a typical run the user
chooses form the main menu the desired clonal  and  environmental
conditions,  specifies  the  beginning  and  ending  date for the
simulation, and selects  the  screen  and  printer  reports to be
generated during run.  Once all initial conditions are specified,
the user selects RUN  SIMULATION  from  the  MAIN  MENU  and  the
program  control  passed  to the SIMULATE module.  SIMULATE keeps
track of the hours  and  days  and  passes control to HOURSTEP or
GROW modules, as appropriate.  When the ending  date  is  reached
summary  of  reports  are  printed  or written to disk files, and
program control is passed  back  to  MAIN  MENU.  At this point a
graphic representation of the tree may be viewed on the screen or
sent to a plotter for output, in my opinion the graphics are  not
very  clear  nor  very  sophisticated.  Other than this I thought
that this is a very good  model.   It can be used to simulate the
growth  of  poplars  under  varying   environmental   conditions,
simulations   that   would  be  difficult  to  conduct  as  field
experiments, and it is easy  to  use  and  get familiar with in a
short time.  (REVIEW ?: RATING = 7)>

Price,Frank  E;  Vaugham,Virginia   (1989):  Evolve.   (BioQUEST)
[GENETICS, MAC<This is a program that allows you to  experiment
with evolution and to get quick results that are impossible to do
any  other way.  You may control the starting population, overall
population size, natural  selection,  pattern of inheritance, and
migration in a hypothetical population.  It provides you  with  a
practice  of posing evolution questions and trying to use various
strategies to answer these  question.   It  also provide data and
graphs that help answer  the  questions.   Evolve  is  very  user
friendly  and in my opinion a first year college student can gain
an understanding of evolution and natural selection ideas.>


Statgraphics (1991):  Execustat.   (PWS-KENT  Publishing Company,
Boston) [STATISTICS, DOS<This is the most wonderful statistical
software,  I  have  played  with  so  far.   You  can  almost  do
everything without using the  manual.   It  has  wonderful  three
dimensional and two dimensional graphics.  It has all the options
you  can imagine on the axis such as rotating, resizing, etc.  It
is easy to make  your  own  file,  save  files, print files, load
files, etc.  Every time you enter a command, it provides the user
with options for input.  This option  makes  it  where  the  user
cannot enter incorrect data.  It is a good software that could be
used  by  students  or  professionals.  Basically, I did not find
anything wrong with this software,  and  I would recommend it for
anybody.  (REVIEW 1: RATING = 9)

I really enjoyed using this software.   Its  capabilities  seemed
unlimited.   The program is very user friendly, and I was able to
enter my  own  data,  make  three  dimensional  plots, rotate the
plots, and analyze the  data  without  having  to  use  the  help
command  or  consult  the  user  manual.  The commands are always
listed in front of the user, and the user must merely select what
he wants to do and  press  enter.   I was really impressed by the
fact that when the computer as you to input data,  it  gives  you
choices.  For example, it will prompt you to enter a variable and
underneath  it  list  the  possible variable names that you might
select.  I also liked the  fact  that  when you retrieve files it
list the files available to be retrieved.  This  saves  the  user
from  having  to  remember  what he named files or from having to
exit the program and look  in  the directory for data files.  The
graphing capabilities were great.  The program has all  kinds  of
graphs  from  simple  histograms to three dimensional plots where
the user can rotate the  axis.   Another  thing I liked about the
program is that when you select different ways  to  analyze  data
there  is  always  an  interpret  option.   This  option explains
exactly what the data is  telling  you and what everything means.
I think that students  taking  statistics  or  probability  would
really  find  this  software useful.  The program would certainly
help students visualize and analyze  data  while at the same time
being user friendly.  (REVIEW 2: RATING = 9)>


Lo Cascio,NJT (1990): Forecasting  Gene  Frequency.   (Wisc-Ware)
[BIOLOGY,  GENETICS,  DOS <This  is a very simple program in my
opinion that could be written by a freshman or sophomore student.
It has a main menu that gets to three other routines: one to make
a Chi-Square statistical test,  second for genetic projections in
Sickle-Cell Anemia, and the  third  for  genetic  projections  in
hemophilia.   If  you  don't want the output to go to the printer
you must turn the  printer  off  because the output automatically
goes to the printer and you have no choice.   There  is  no  help
menu or command and a lot of other missing options.  Overall this
is not a good software.  (REVIEW 1: RATING = 2)

This  software  is  really  simple.   To  me,  it  merely  offers
explanations about chi-square, sickle cell anemia and hemophilia.
Most  of  the program consisted of written paragraphs about these
subjects.  One  problem  I  had  with  it  was  the  fact that it
automatically prints everything when ever you  press  an  option.
This  is really unnerving.  There are very few options concerning
saving data or manipulating data or error messages.  For example,
if you incorrectly enter a value you get an error message that is
dealing with the  program,  and  you  don't  receive a message to
re-enter a value or that the value is not within a correct range.
The program is too simple to be of much use, but it could be used
by practically anyone.  In my opinion,  the  program  would  have
very  little  to offer a user except for information about sickle
cell anemia or hemophilia.   (REVIEW  2:  RATING  = 2) For review
refer to THE QUARTERLY REVIEW OF BIOLOGY June 1991 volume 66 page


Calley,John;   Collins,Angelo;   Jungck,John   (1990):   Genetics
Construction Kit;  A  project  BioQUEST  simulation.   (BioQUEST,
Biology  Dept.,  Beloit  College,  Beloit,  WI  53511)  [BIOLOGY,
GENETICS, MAC<This program is very good at allowing the user to
cross organisms in order to determine the inheritance patterns of
a  particular  trait.  The program did a good job of allowing the
user to decide how to cross organisms.  For example, the user can
decide whether to cross two organisms which have the same genetic
make up or cross two  random  organisms.  Also, the program keeps
track of which crosses have been made and in which vial these are
stored.  This aspect of the program is  real  handy,  because  it
helps  the  user keep track of what he has done while at the same
time helping him locate previous  crosses.  Another aspect of the
program that made it easy to use was the fact  that  the  program
counts  for  the user, and the user is able to decide if he wants
to see the total number of  organisms  with a certain trait or if
he wants to see the number of each sex with a certain  trait.   I
also  found the data to be realistic, because on some simulations
it took a couple of  crosses  before any conclusion could be made
about the organisms inheritance.  This is very  similar  to  what
could  occur  in  a real lab.  There was only one thing I thought
the program should  have  included.   That  is  I think it should
display ratios.  Since the program  counts  and  classifies  each
generation,  I  think  it  should  also  demonstrate a ratio.  It
certainly would help the student decide what alleles are present.
However, in general I think the program is a good simulation of a
real lab  where  students  start  with  organisms  they know very
little about and try to draw conclusions about their  inheritance
by crossing them.  In fact this may be better than doing the real
lab,  because  it  allows  the student to cross organisms and get
results in a fraction of the time.  (REVIEW 2: RATING= 8) (REVIEW
1: RATING = 8)>

(1990): Isolated  Heart  Lab.   (BIOQUEST,  Biology Dept., Beloit
College, 700 College street, Beloit,  WI  53511)  [BIOLOGY,  MAC]
<This  program  is designed to allows the user to conduct his own
experiment in order to answer  the question, "Does cardiac output
change with heart rate?  inotropic state?  peripheral resistance?
or preload?" Within the lab itself the user  is  able  to  choose
which  of  these  four  things  he wants to experiment with.  The
choices include: diastolic function, systolic function, afterload
effects, effects on  heart  rate,  or  tutorial  problem.  When a
choice is made the user can edit the input in any manner he wants
in order to see how this will affect cardiac output.  The program
is user friendly in the fact that it highlights  the  input  that
the user is able to change.  Once the information has been edited
you  can  begin  the  experiment.  The user can select start, and
then the program will graph  information as the data changes over
time.   The  user  can  stop  the  program,  or  it   will   stop
automatically after a given time.  The program gives the user the
option  of  what  s/he  wants plotted.  The choices include: left
ventricle  pressure  and  volume   versus  time,  left  ventricle
pressure versus volume, or left ventricle pressure and  arteriole
pressure  versus  time.   The  program  also  allows  the user to
perform several trials.  The program  in general is user friendly
because commands are easily understood and  performed  using  the
mouse.   However,  I  was not able to figure out how to print out
information or if that option is even available.  Besides the lab
itself, the program has  an  Isolated  Heart Lab Introduction.  I
thought this was very nice.  This part of the  program  includes:
an  introduction  (which gives definitions and the purpose of the
software), the heart  plumber's  kit  (which  allows  the user to
perform a bypass in which the user selects whether  he  wants  to
use a valve, ventricle or vessel in each of four spots), pressure
time  animation (which shows an EKG at the same time it shows the
heart pumping with a  description  of  each movement and the user
can hold the mouse down to see continuous pumping or go frame  by
frame  to  understand  each  section), and a pressure volume loop
animation (which does the same  thing as pressure time animation,
but also includes a volume graph).  This part of the program  was
the  most  impressive  because the frame by frame descriptions of
the heart pumping allows  the  user  to visualize what exactly is
happening while reading about it.  In my opinion,  this  software
would  really  be  useful to someone who is studying this subject
matter.  I was able to learn a  lot of things just by running the
animations, and I feel that someone who is studying this material
could learn even  more.   Overall,  it  is  a  friendly  software
especially  if  you  understand  the  subject matter.  (REVIEW 2:
RATING = 9)> <The heart  lab  is an excellent simulation of heart
function.   The  simulation  enables  one  to  explore  how   the
ventricles  of  the  human  heart performs as a blood pump and to
characterize changes that alter  its performance.  The program is
so simple to use that even those with very  little  knowledge  of
the  physiological function of the heart may find it educational.
The program  does  on  graphs  what  a  textbook  does in several
chapters.  The simulation is very widespread in  its  variations;
it  seems  to  answer almost any question one may have concerning
the function of the  heart.   Although  heart lab is informative,
the graphs are dull.  The program could be more exciting  if  the
diagrams  were  more life-like.  Watching the same graphs tend to
become boring after a  period  of  time.   A life-like heart with
actual movement would have made this program superb.  If it  were
just  cartoon-like,  it  would  be  even  simpler to use and more
exciting to watch.  Using the program is probably the closest one
can get to hands on  experience  in  the area of cardiology other
than working with  patients.   The  program  still  provides  one
simple  advantage  over  working  with  patients  and that is the
ability to experiment with  different variables and get immediate
results.  Such a  program  as  Heart  Lab  might  be  used  as  a
reference  to physicians or medical students when examining heart

[MACINTOSH,  STATISTICS,   REGRESSION].<This   is   a  statistics
package.  It is very useful for basic level statistical analysis.
The program comes with a spread sheet with  allows  the  user  to
input  data  without  exiting to program.  The program makes very
nice plots.  The package will also  do regression and some of the
simpler  tests,  e.g.,  the  t-test.   There  are  many  examples
included with this program.  The manual is also easily  read  and
understood.  The biggest problem is that the information does not
fit   on  the  screen.   It  is  slightly  annoying  to  have  to
continually more  the  screen  around  to  see  what doesn't fit.
Overall, this is a very  good  introductory  statistics  package.
(Review 3: Rating 7)>

Levitan,Herbert (1988): LOGISTIC.  (Wisc-Ware) [BIOLOGY, ECOLOGY,
SINGLE  POPULATION,  DOS-WINDOWS <This  program is based on the
simple logistic differential equation.  It is a very easy program
to use with Windows (which  has  nice  graphics) and a mouse.  It
gives you the option to change I.C.  and other  parameter  values
in  the  equation.   There  is  no print out option, but there is
nothing much to print since all  you  have is one window which is
half data and the other half is for plotting the data.   However,
the  software  serves the objectives of the author.  One of these
objectives is to encourage  students  to use computer simulations
as a tool for learning.  I  think  that  this  objective  is  met
because  of  the  simplicity  of  using  this program.  Hopefully
students will be encouraged to use other simulation programs that
may be more involved after  using  this  one.  The program has an
example of the discrete logistic chaos graph that students may be
interested in seeing, and also students can input data that makes
a population go extinct.  Overall, this is not a very complicated
program; however, the author does mention that  it  is  based  on
simple logistic equation.  (REVIEW 1: RATING = 6)

The logistic software is very simple to use.  The fact that it is
used with Windows makes options easily accessible, and also makes
everything easy to see.  The program itself is real simple and is
easily  understood.   I  liked  the  fact that it is very easy to
change data, and if you plot one  set of data you can leave it on
the screen and compare it with the next group of data  you  enter
and  plot.   However,  in general the software seemed very simple
and limited in  its  applications.   In  my  opinion, the program
would be easy for anyone to use, but would be of  little  use  to
someone because it is limited in what it does.  (REVIEW 2: RATING
= 4)>

Maddison,Wayne  P;  Maddison,David  R (1993): MacClade.  (Sinauer
Associates, Inc.  Publishers,  North  Main Street, Sunderland, MA
01375) [ECOLOGY, MAC,  MODELING <MacClade  is  a  program  that
provides  theory  and  tools  for  the  graphic  and  interactive
analysis  of  phylogeny  and  character  evolution.   The program
reconstructs and displays character evolution on the phylogenetic
tree, and, as the user  manipulates  the tree on screen, MacClade
gives feedback via tree graphics, statistics, and charts.  Latest
version is 3. This package contains some  very  interesting  AIDS
information   as  the  sample  data.   The  package  is  somewhat
confusing for how to use it.  (REVIEW 3: RATING 4)>

John  H.  Hubbard;  West,Beverly  H  (1992):  MacMath.  (MacMath,
SINGLE POPULATION, MAC<The  software was designed to supplement
a junior or senior level class in differential equations.  I,  as
a  junior,  found  the  software  easy  to  work with and easy to
understand.  It is very  useful  as  a tool to graph differential
equations in two or three dimensional space.   When  I  used  the
software  with  the  manual,  I  was  able  to create really neat
examples.  What I liked  about  the  program  is  that it is very
versatile.  The fact that it combines  several  programs  in  one
would  make  it  a  useful  tool  that  could be used for various
classes as an undergraduate.  In  my opinion, this software would
definitely be very helpful and easy to use for an  undergraduate.

This   software  can  only  be  used  for  class  demos  and  for
undergraduates in  general.   It  has  several  separate programs
which include an analyzer which graphs  a  general  function  and
finds  its roots, differential equations which have two and three
dimensional aspects with phase planes, a demo for bifurcation, an
eigenvalue and eigenvector  solver  program,  a numerical methods
program for solving differential equations (Runge  Kutta,  Euler,
Midpoint  Euler),  Fourier  approximation for any given function,
and others which are  not  important for our discussion.  Because
this is a Mac program, it  is  very  simple  to  use,  everything
except  input  of  data  can be done with the mouse.  The thing I
liked the best was  its  eigenfinder program.  This program gives
the output in a very nice mathematical  manner;  however,  it  is
limited  to  twelve  by  twelve  matrices.   In  the  phase plane
program, you can start the  trajectory  any place you want on the
screen by pointing the  cursor  and  clicking  the  mouse.   This
aspect  is  a time saving device because the user doesn't have to
plug in initial conditions.   The three dimensional graphics were
not very good.  However, it serves the purpose in  which  it  was
intended.  (REVIEW 1: RATING = 8)>


Myers,Gene; Blanco,Carlos; Jahnke,Jerome; Hallick,Richard (1990):
MacMolecule.   (University  of  Arizona)  [CHEMISTRY,  MAC<This
program takes organic molecules and  provides the user with a 3-D
model of the structure.  The  program  has  a  complete  list  of
molecules  that  are very common in chemistry.  All the user must
do is select  the  molecule,  and  the  program  provides a three
dimensional representation of the molecule.  Once you are viewing
the model, there are other options that  can  be  selected.   The
program  will  allow you to rotate the model in any direction you
want by simply taking the  mouse  and  clicking it in the desired
direction, the computer will continuously rotate the molecule  in
any  direction  you choose until you indicate to stop, or you can
indicate in which direction you want light rotated.  This program
is really user friendly in the fact  that all the user must do is
click the mouse on the model s/he wants to use  and  then  select
the  options  s/he  wants  to  perform  (all  of which are easily
understood).   There  were  only  two  problems  I  had  with the
program.  One is the fact that  the  model  represents  different
elements  within  the  compound  with  different  colors  without
indicating  what color goes with what element.  Also, I think the
program should include  an  empirical  formula  for the compounds
being graphed.  Besides these problems the program does  a  great
job  of  demonstrating compound in three dimensions.  I feel this
program would be of great use to students who are trying envision
compounds in their minds.  The software is certainly a lot easier
to use than  the  model  building  kits  currently  being used in
chemistry classes.  In my opinion, this program would be of great
use to someone  studying  chemistry  or  learning  about  organic
molecules in biology (e.g.  DNA).  (REVIEW 2: Rating= 8)

This  software  is  designed  for teaching molecular structure to
students of biology, chemistry and allied fields.  It begins with
discussion of small  biological  molecules  such  as amino acids,
lipids,  nucleotides,  sugars,  and  vitamins.   Then,  this   is
followed  by  larger molecules such as DNA and RNA.  Students can
use data  from  molecular  structure  data  bases  and create 3-D
models of small and large molecules on  computer  screen.   Users
are able to interactively rotate the image in the x, y, z axis on
the  computer  screen.   The  images  can be saved to a disk as a
sequence of PICS images that  can be replayed from MacMolecule as
an animation sequence.   Very  nice  images  and  rotation,  user
friendly software.  (REVIEW 1: RATING = 8)

Very nice graphics.  Well-written program. (Review 3: RATING = 8)>

Chariot  Software  Group  (1988):  Math  1.  (CSG  Pub Domain/ SW
library) [ALGEBRA, MAC<I played  with this software for over an
hour.  It has a lot of options when they work.  The  things  that
work  correctly are the 2-D graphs, the fractal, the Mac Lin 1.0,
and the tangent  options.   I  managed  to  crash  the 3-D graphs
several times on different easy functions like z= x**2 + y**2 for
example.  I managed to crash the conformal maps option, and I was
unaware of what I did to make the program crash.  In other words,
the program is in need of a  lot  of  fixing  and  modifications.

Chariot  Software  Group  (1988):  Math  2.  (CSG  Pub Domain/ SW
library) [ALGEBRA, MAC<This  is  a  simple program.  The option
MathMaster is designed to solve first year algebra problems.   It
has  an  equation editor to create integral summations, fractions
square roots and  matrices.   It  has  a number investigator that
gives information on integers up to twelve digits such  as  prime
factors,   hexadecimal   equivalents,   and  binary  equivalents.
Scientist's helper is data  analysis  / graphing program.  Simple
graphing,  data  reduction,  multiple   regressions,   filtering,
Fourier transform, etc.  are also available.  (REVIEW 1: RATING =

McDonnell,Eon (1990):  mDNA.   (intellimation,  P.O.   Box  1922,
Santa  Barbara,  CA  93116-1922.)  [BIOLOGY, GENETICS, MAC<This
program provides a student  with  a  tool for exploring different
mitochondrial DNA models.  The student gives the  initial  values
s/he wants such as population size, number of generations, length
of  an  individual  (up to 400 sites), and the restriction enzyme
used.  In the simulations,  family trees are continuously updated
to show current inheritance structure.  The student  is  able  to
pause  the  simulation at any time to show DNA, highlight similar
groups, or inspect mutations.  One can save pictures or data to a
file for later use,  but  this  file  cannot be printed out using
MacPaint or similar software.  Over all, this is a  good  program
and  has  a good help facility to help get you going.  (REVIEW 1:
RATING = 6 ) (REVIEW 3: RATING = 5)>

Calley,John; Jungck,John (1990):  Microbial Genetics Construction
Kit  (BIOQUEST  Software).   (BioQUEST,  Biology  Dept.,   Beloit
College, Beloit, WI 53511) [BIOLOGY, GENETICS, MAC<This program
was  designed  to  allow  students  to  perform  experiments with
bacteria to simulate  experiments  that  might  be performed in a
real lab.  The software begins by giving the user  a  main  menu.
Here  the  user  can  choose one of five options: Serial Dilution
Tour (which is designed to allow the student determine the number
of bacteria in  a  random  sample), Phenotype Identification Tour
(which allows the user to determine the phenotype of the bacteria
based on replication), Complementation  Tour  (which  allows  the
user  to perform experiments to decide if two organisms that need
the same nutrient to  grow  can  benefit each other), Conjugation
Tour (which allows the user to conjugate a colony) and Full  Menu
(which  includes  all  of  the  options  above).  This menu is in
increasing order of difficulty.   For  example,  if you start off
experimenting with the  Serial  Dilution  Tour  and  master  this
section,   then   you   select   the   next   option   (Phenotype
Identification  Tour)  it builds on the first option.  This would
be very helpful to  a  first  time  user who could gradually work
his/her way through the experiments and by the time s/he  chooses
the  Full Menu option, s/he would be familiar with everything the
program has to offer.  In  the  Serial Dilution Tour, the program
provides the user with a test-tube of unknown bacteria.  The user
must dilute the test-tube until s/he is able to count the  number
of colonies that are present.  I liked the fact that the computer
keeps  track  of the power to which you have diluted the bacteria
and the fact that if you select the test-tube history option, the
computer  will  tell   you   information  about  that  particular
test-tube.  In Phenotype Identification Tour the  computer  gives
you  a petri dish with colonies.  The user can then replicate the
plate and choose which nutrient  or antibiotic s/he wants present
on the new media.  In this section,  the  Media  Matrix  and  the
Phenotype  Worksheet  make  it  easy to view what experiments you
have performed.  The matrix indicates what nutrient or antibiotic
is available on which  petri  dish  and  the worksheet allows the
user to input his/her own data (s/he  indicates  whether  or  not
s/he  has  found  each  nutrient necessary or not and whether the
bacteria is  sensitive  to  each  antibiotic.)  To  me, these two
options make it very  easy  to  keep  track  of  experiments  and
conclusions.   In  the  Complementation Tour the same options are
available as  before  but  now  the  user  is  also provided with
complementation worksheet for  which  the  user  indicates  which
nutrient  s/he  is working with.  Also, there are several options
that let the user decide if  he  wants to inoculate a tube with a
colony on the same media or different media or plate  a  tube  on
the  same media or different media.  In the Conjugation Tour, all
other options are available, but  now  the user can conjugate two
colonies.  In general, I found the experiment realistic,  because
it took several experiments before any conclusions could be made-
just  like in a real lab.  Also, the computer leaves it up to the
user to  make  conclusions-  just  like  in  a  real  lab.  In my
opinion, this software would be simple  for  someone  who  had  a
knowledge  of a MacIntosh and would also help educate the user on
the subject matter.  (REVIEW 2: RATING = 8)>

Salmon,I (1986):  MicroModeller.   (IRL  Press (Oxford University
Press), Oxford) [ECOLOGY, POPULATION, DOS<For review  refer  to
THE QUARTERLY REVIEW OF BIOLOGY March 1990 volume 65 page 131>

Lapidus,Martin  (1990):  Models.  (Lascaux Graphics 7601 N. Calle
Sin  Envidia  #31   Tuscon,   AZ   85718)  [CALCULUS,  DIFFERENCE
nice software for solving  difference and differential equations.
I found it to be very fast.  In fact, I have tried  a  difference
equation  that  was  implemented first on Mathematica (not in the
most efficient way),  and  Models  was  much  faster  and easy to
implement.  We got to see the two and three dimensional  graphics
easily  and  nicely,  and we had the option to zoom in and out on
any part of the  graph.   I  liked  the  ability of being able to
rotate the axes and the fact that it is able  to  solve  a  large
system  of  equations unlike Populus which could handle a maximum
of four equations.  This software also allows you to set the step
size for integrating the  ODE,  which  is something that comes in
handy when you know  some  information  about  the  ODE  you  are
modeling.  One disadvantage is that if you have a large system of
ODEs  that  can  be  defined  iteratively using a DO LOOP then it
would be  tedious  to  use  models  because  you  must enter each
equation separately.  In my opinion, this was  one  of  the  best
software  programs  I played with (for DE's).  I highly recommend
this for junior or senior  level students, graduate students, and
professionals.  (REVIEW 1: RATING = 9)

The program is a  very  good  tool  to  help  students  visualize
difference  and differential equations.  The software overall was
simple  to  use  and  would  require  very  little  knowledge  of
computers.  The only problem I  had  with  the package is that it
was difficult to use without a mouse.  When used on a computer in
which I could use the keyboard only,  I  found  it  difficult  to
figure  out  how to do different things.  However, when the mouse
was available, the program was  easy  to use, and I enjoyed using
it.  In my opinion, Models is a very easy to use  software  which
would  certainly  be  useful  to students in at any level who are
dealing with difference  and  differential equations.  (REVIEW 2:
RATING = 9)>

Press,William   H;   Flannery,Brian    P;    Teukolsky,Saul    A;
Vetterling,William   T  (1988):  Numerical  Recipes.   (Cambridge
University Pres,  Cambridge  and  New  York) [NUMERICAL ANALYSIS]
<For review refer to THE QUARTERLY REVIEW OF BIOLOGY  March  1989
volume 64 page 115.>

McKelvey,Kevin;    Crocker,Jennifer   (1992):   OWL.    [BIOLOGY,
GENETICS,  DOS,  MODELING <A   spatially  explicit  system  for
modeling demographics and genetics  of  the  spotted  owl.   This
modeling  system consists of five individual program which allows
you to create a map  of  a  specific land configuration, to place
owls, to modify the rules that  govern  model  behavior,  and  to
produce condensed output.>

Curtis,Dave  (1990): PEDRAW.  (Academic Department of Psychiatry,
St Mary's Hospital Medical  School  Praed  Street, London W2 1NY,
England,  e-mail  [log in to unmask])  [BIOLOGY,  GENETICS,   DOS]
<PEDRAW  is a program which draws out family trees in either text
or graphics  mode.   It  is  designed  to  be  used  to help with
genetics research, especially linkage analysis using the  LINKSGE
and  LINKSYS  packages.  Data about the structure of the pedigree
and about the individuals within it  is  read in from a data file
which can have one of a variety of formats.   One  individual  is
selected    and    his/her   relatives   are   displayed   either
diagrammatically using shaded  symbols  or  else as paragraphs of
text linked by the IBM box character set.  The pedigree is  saved
to disk in either Microsoft Paint Format or as a text file.>

Will,Ed   (1987):  Plant  Kingdom.   (HyperCard)  [BIOLOGY,  MAC,
TAXONOMY<This program  is  very  similar  to the Animal Kingdom
program.  It has the same problems.  It has more  than  just  the
Plant  kingdom.   There are also fungi and some algae.  The basic
problems remain that the  program  is  not very user friendly and
that there seems to be a very limited application for the use  of
this program.  (REVIEW 3: RATING = 4)>

Wilkinson,HT;  Pederson,WL;  Pondy,K  (1989):  Plant  Root Model.
(Wisc-Ware) [BIOLOGY, ECOLOGY,  PHYSIOLOGY,  DOS <A very simple
program that has only two screens- one for changing data and  the
other  is a screen for the graph of the volume of the rhizosphere
where you can see it  in three different directions (upper, side,
skew).  In the data screen you can change  the  biology  and  the
edaphic  factors  in  the  soil  which  in  turn  changes the max
distance that  the  fungus  can  grow  to  the  root  and infect.

This program is very simple and is very specific.   In  order  to
use  this  software,  the  user  would  have to want to observe a
rhizosphere otherwise the program  would  be  useless.  I did not
like the fact that it simply showed you a sphere  around  a  root
with  no  reference  to  distance  or  why it gets smaller if you
change certain factors and larger  if you change others.  Even if
the  user  changes  the  influence,  there   are   very   limited
possibilities,   thus  making  the  software  useless  after  all
combinations of influences have been  observed.  The only thing I
liked about the program was that it had a good explanation  about
what  rhizospheres  were,  and it was simple to use with windows.
In my opinion,the software  would  not be beneficial to students.

Etter,Ron; Maddison,David  (1992):  PopDyn.   (EcoSoft,  Inc.,  7
Noble  Hill,  Beverly,  MA  01915).   [BIOLOGY, ECOLOGY, MULTIPLE
seemed to be designed to demonstrate  the  graphs  of  population
dynamics.   The  program does not allow the user to use their own
equations, it simply allows the user to adjust constants.  To me,
this type of program is not  very useful, unless a student wanted
to see the graph of general logistic, exponential,  predator-prey
or  competition  equations  and  even  then  once you've seen the
equation there is nothing  really  else  to see.  The graphs were
cute, and it was really easy to change the parameters so it is  a
very user friendly program.  Other options in the program include
looking  at  different  models in three dimensions.  This part of
the program again showed  really  colorful and pretty graphs, but
the graphs lacked explanation.  It was really easy to rotate  the
axis  of  the graphs, but you cannot rotate the graph itself when
you rotate the axis.  Instead, the current graph is automatically
erased and the user must redraw  it.   To me, it was difficult to
visualize the graph because it did not rotate when the axis  did.
Also,  the  program  has  a  group of files that you can look at.
These include great pictures  that people obviously have created,
but again there is no explanation or equations that the user  can
relate  these  graphs.   Instead,  they  just  seem  to  be  nice
pictures.   In  my opinion, this program has very little to offer
students, unless they just want  to see demonstrations of general
population dynamics equations.  (REVIEW 2: RATING =4)

This software is designed for demonstration  purposes  in  class.
One  of the things I enjoyed very much is that in the competition
model, the user is  able  to  move  the isoclines anyway he wants
which allows him to  change  the  parameters  and  thus  changing
equilibrium  and  then it allows you to see the phaseplane of the
two species.  However, it  is  limited  in  the sense that it has
only   four   models   exponential,   logistic,    Lotka-Volterra
predator-prey  and  competition models.  One thing I did not like
about the program is that it does  not allow you to edit or enter
equations.  It has a nice chaos demo of predation and competition
three dimensional model.  The graphics are nice.  It is very good
software for somebody who has a course in differential  equations
(sophomore or junior level).  (REVIEW 1: RATING = 7)>

This  program  is  nicely done and easy to use.  The read me file
gives a good description of the package.  (REVIEW 3: RATING = 7)>

Berryman,Alan A; Millstein,Jeffrey  A (1988): Population Analysis
System  (POPSYS).    (Ecological   Systems   Analysis,   Pullman,
review refer to THE QUARTERLY REVIEW OF BIOLOGY March 1990 volume
65 page 130>

Towner, H.: Population Ecology And Genetics.  [ECOLOGY, GENETICS,
OF BIOLOGY September 1992 volume 67 page 425>

POPULUS.  The Populus  software  contains  a  set  of  simulation
models   that   we   use   in  teaching  population  biology  and
evolutionary ecology at the University  of Minnesota.  All of the
simulations share a common format, as follows: After a  model  is
chosen  from  the menu, the program displays (optionally) several
screens of background  material  which  introduce the mathematics
and end with basic references.  Next, there is a  screen  listing
all  of  the  input  parameters;  students  can  move  among  the
parameter  boxes  and  change initial defaults to values of their
own  choosing.   The   program   maintains   a  record  including
permissible maxima and minima  for  each  parameter  and  filters
input  values  accordingly.   Usually  there are several possible
outputs (e.g., N vs T graphs  and phase planes) which can also be
selected from the parameter input screen; alternatively, students
view the different outputs in sequence, by pressing the space bar
between views.   Context-sensitive  help  screens  are  available
(press  <F1>)  from  the input and output screens of every model,
and by pressing <F1> twice one  can see a menu of additional help
screens that include discussions  of  function  and  editing  key
assignments implemented by the program, printing protocols, video
options, etc.

Hardware Requirements

Populus  is written in Borland Pascal 7.0 to run under DOS on IBM
and  compatible  computers.    The   program   is  offered  in  a
protected-mode version for  computers  with  286,  386,  486,  or
pentium  microprocessors and 2 MB RAM.  There is also a real-mode
version  for  XT  class  computers  with  the  8088  chip.   Full
implementation of Populus in  real  mode  requires about 500KB of
RAM,  free  of  memory-resident  utilities  and   drivers.    The
real-mode  program  will  use  LIM  expanded memory, reducing the
frequency of disk reads and speeding program execution.  Although
the code will emulate an xx87  coprocessor if one is not present,
many of the models are computationally  intensive  and  will  run
much more rapidly on a machine with the floating-point chip.

       Version  3.4  will  run on any IBM-compatible video system
that  permits  graphic  displays,  including  "Hercules,"  "CGA,"
"EGA," "VGA," and  "IBM8514."  There  are  also  VESA drivers for
800x600, 1024x768, and 1280x1024  pixels.   In  most  cases,  the
software   will  recognize  and  accommodate  your  video  system
automatically.  If your display emulates one of the color systems
in shades of gray (as many LCD screens do, with varying success),
consider using the option  which  forces output to the monochrome
mode.  The IBM8514 system is detected as  VGA  by  Turbo  Pascal;
IBM8514 users who desire full 1024x768 resolution can select that
video  mode  from  the  Populus  Options  Menu (Alt-O) and save a
populus.cfg file to  disk  so  that their preferred configuration
loads automatically each time the program is run.

      Populus 3.4 contains a set of commercially produced drivers
by  Ryle  Design  that  supports  a  wide  variety  of  printers,
including 9-pin and 24-pin dot matrix printers, HP laserjets  and
deskjets,   the   HP  paintjet,  and  printers  implementing  the
Postscript page-description language.   Print  files  may also be
saved to disk and sent to the printer later using the  DOS  Print
command.   Set  the  appropriate  printing  configuration  on the
Populus   options   menu.     Note   that   Postscript   supports
graphics-mode printing only.  Our introductory narratives and all
outputs are rendered in graphics mode, but the  parameter  inputs
and  help  windows  are  text  mode  screens.  To print them on a
postscript laser printer you  will  have  to  set  it up as an HP

Bells and Whistles

       For many problems  and  exercises  it  is  desirable  that
students  be  able  to  read numerical values accurately from the
graphical output.  We  have  included  several new video routines
for this purpose.  A  gridding  function  (press  <Alt-G>)  plots
horizontal  and  vertical  lines from the major axis ticks, and a
second <Alt-G> grids the minor  ticks.  A third press toggles the
feature off.  Our video zooming function (press <Alt-Z>) pops  up
a  rectangle whose corners can be moved (with the cursor keys) to
any point  on  screen.   Pressing  <Enter>  then  zooms  this new
rectangle to full-screen size.  By zooming in on  an  interesting
equilibrium region and gridding the output, final frequencies can
be read with any desired degree of accuracy.

       For   many   time  trajectories  of  ecological  dynamics,
comparison of arithmetic  and  logarithmic  plots has pedagogical
value.  Populus plots arithmetic time trajectories by default but
allows you to toggle a semi- logarithmic  plot  (press  <Alt-L>).
Like  other video utilities in Populus, the feature is turned off
(and the screen-bottom  options  line  is  cleared) with the same
<Alt-L> keystrokes that turned it on.

       Populus models that display <F4> in the lower-right corner
of their input window include a  routine  that  allows  on-screen
comparison  of  outputs  resulting  from  two  different  sets of
parameter values.  To implement this feature, simply toggle <F4>.
Graphical  output  from  the  current  parameter  values  will be
plotted in the normal colors, while output of  the  previous  run
will  be  shadowed  in black.  A second press of <F4> toggles the
graphical comparison routine off.

       Stability analyses are  important  in  helping students to
understand the dynamics of ecological  and  evolutionary  models,
and  we  have  provided a rich set of stability tools in Populus.
Many of the  genetical  simulations  begin from several different
starting  gene  frequencies  automatically.   Optional  stability
analyses are  also  available  with  the  phase-plane  graphs  of
ecological  dynamics.   To  implement this feature, press <Alt-S>
after a phase diagram is complete;  a  cursor will pop up and can
be moved to any point on the screen.  Pressing <Enter> will  then
initiate  a  trajectory  from that point, and the dynamics can be
run forward or  backward.  Alternatively, multiple-starting-point
stability analyses may be run by pressing <m> after <Alt-S>.  The
program will then initiate trajectories  from  the  perimeter  or
from  a  gridded  pattern  of  points (the number and position of
starting points is set from  the  options menu) to illustrate the
stability of internal equilibria.

       In addition to these video utilities, Populus now includes
several file- handling routines.  Output data  from  any  of  the
simulations   can   be   saved  to  disk  for  analysis  using  a
spreadsheet, statistical package, or  graphics editor.  To do so,
call up the options  menu  after  running  your  simulation,  and
specify  a  path and name for your data file.  Similarly, Populus
can save to disk and  reload  sets of model parameter values; you
might use this feature to save a series of parameter  files  that
show  particularly instructive examples, and ask your students to
load, run, and analyze them as part of a lab exercise.

Finding Documentation

       This file contains only  a  brief introduction to Populus.
Full descriptions of each feature and a listing of the keystrokes
necessary to call and implement it are built  into  the  program,
and  are  accessible  from the Main Help Menu.  To see this menu,
press <F1> (or if you are  already  in one of the model parameter
or  output  screens,  press  <F1>  twice,   to   get   past   the
context-sensitive  help).   We  recommend a tour of the Main Help
Menu  as  the  quickest  way  to  familiarize  yourself  with the
capabilities of Populus.

Sponsorship and Distribution

      This software is underwritten by the  Undergraduate  Course
and  Curriculum  Development  Program  of  the  National  Science
Foundation (USE-9150887, USE-919155967, DUE-9354777); it is not a
commercial  venture and we encourage you to distribute it without
charge to any colleague or student  who  will put it to good use.
If you find a bug please tell us.  We will fix it and provide you
with an update.

                              Don Alstad Department  of  Ecology,
                     Evolution & Behavior University of Minnesota
                     1987  Upper  Buford  Circle  St.   Paul,  MN
                     55108-6097                      612-624-6748
                     [log in to unmask]


     There  are  now  two  versions  of  Populus  posted  on  the
Minnesota    Ecology    Server    (,    IP   A  protected-mode  version  for  286  and later
microprocessors  with  2MB   RAM   is   compressed  in  the  file
pop34P.exe.  A real-mode version for older XT-class computers  is
compressed in the file pop34R.exe.

     In  addition  to  this,  the protected mode version
contains five files as follows:

1) Populus.doc is an ascii  text  file that explains features and
requirements of the software.  We suggest that you read it before
using the program.  Note that full documentation is  an  internal
part  of  Populus, accessible from the main help menu (press <F1>
once, or  twice  depending  on  context),  and  that many program
features are adjusted from the Options Menu (press <Alt-O>).

2) Populus.exe is  the  binary  executable  file  that  runs  the
protected-mode  version;  it  should  be placed in the hard-drive
directory that you will use when running Populus.

3)  Populus.txt  contains  all  of  the  text  screens  that  are
displayed by Populus.  Populus.txt is indexed for rapid retrieval
to screen, and is not  an  ascii  file;  you  will not be able to
simply dump it to a printer.  If  you  would  like  to  print  an
introductory narrative, do so from within the populus program.  I
will   make   expanded   versions   of   these  narratives  (with
illustrating graphics  and  suggested  exercises)  available in a

4) DBMI16BI.ovl is a DOS Protected Mode Interface Server that  is
required  for  Populus  to  run  in  the  protected mode.  We are
licensed by Borland  Internation-  al  to  distribute it with our

5) RTM.exe is a  run-time  manager  that  loads  Populus  in  the
protected  mode and provides a protected mode memory manager.  It
is also a Borland  product.   All  six  of  these files should be
housed together in the  same  directory,  or  linked  by  a  path
command.   To  run  the  protected-mode  Populus,  type "populus"

     The real-mode  version  of  Populus  includes  four files in
addition to this, as follows:

1) Populus.doc serves both  Populus  versions  and  is  described

2)  Populusr.exe  is  the  binary  executable  file that runs the
real-mode  version;  it  should   be  placed  in  the  hard-drive
directory that you will use when running Populus.  Note the extra
letter r in the file name, for "real-mode."

3) Populusr.ovr contains the overlays that swap different  models
and  routines  in  and  out  of  computer  memory.   This file is
required to run the program.

4) Populus.txt  is  used  by  both  versions  of  Populus, and is
described above.   All  six  of  these  files  should  be  housed
together  in the same directory, or linked by a DOS path command.
To run the protected-mode Populus, type "populusr" <enter>.

     Populus  allows  you  to  save  other  files  to  disk.  For
example, if you  elect  to  preserve  any  of  the  configuration
information  chosen  from  the  Populus options menu, the program
will save  a  populus.cfg  file  and  your  configuration will be
loaded automatically each time Populus starts.   Parameter  sets,
print  files,  and  data outputs may also be saved with filenames
(*.par, *.prn and *.dat)  of  your  choosing,  but only the files
listed above are necessary to run the program.

     We encourage you to give this software without charge to any
students or colleagues who will put it to good use.  When you  do
so,  please  pass  on  the entire protected- or real-mode package
intact.  File sizes should be as follows:

                   populus.doc  8347  bytes  populus.exe  1070080
                   bytes populus.txt  838959  bytes 4578
                   bytes DPMI16BI.ovl 65376 bytes RTM.exe  108846
                   bytes  populusr.exe  110624 bytes populusr.ovr
                   878107 bytes

If the file sizes that you receive differ from these values, your
copy is corrupt and should be destroyed.

      We  will  maintain  current   copies   of  Populus  in  the
/pub/populus  subdirec-  tory  of   for
anonymous  FTP.   Users  who  leave an email address as requested
will be notified when a new version of the program is posted.  If
you lack the facilities to  acquire Populus over the internet, we
will provide you with a disk by snail mail for $10 payable to the
University of Minnesota.  Write  to  Don  Alstad,  Department  of
Ecology,  Evolution  and  Behavior, University of Minnesota, 1987
Upper Buford Circle,  St.   Paul,  MN  55108-6097.  Please do not
send purchase orders.

Ferson,Scott; H. Resit  Akcakaya  (1991):  RAMAS / AGE.  (Applied
Biomathematics  100  North  Country  Road  Setauket,  NY   11733)
software serves a  very  specific  purpose.   The  purpose of the
program is to model a single population based on various  factors
that  affect the population's growth and development.  If this is
the sole purpose of  the  user  then  the  software would come in
handy, and the graphs would prove helpful  in  demonstrating  the
relationship  between  various  factors  and  each age group.  If
someone had a  lot  of  information  about  a single species, the
software would  be  useful  in  relating  the  information.   The
problems  I  had with the program are it could not be used easily
without a manual, it  is  not  very  practical to use to simulate
arbitrary situations, and it is  not  very  informative.   In  my
opinion the program would only prove to be useful if the user has
knowledge  of  age-structured  population  dynamics  and wants to
relate information on  a  specific  example.   For another review
refer to SCIENTIFIC SOFTWARE winter 1991-1992 page 5.>

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